<div dir="ltr">In theory this should work, but the <a href="http://gtf2vep.pl">gtf2vep.pl</a> script doesn't seem to work too well with this particular GFF (it was designed really to work with GFF/GTFs as produced by Ensembl or NCBI). Probably with some tweaks it could be made to work - I believe the major issues are caused by features being out of the order that the script expects.<div><br></div><div>The new code uses a much more robust system for constructing transcripts and has been tested with GFFs from Ensembl, NCBI and GENCODE.</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 27 September 2016 at 13:22, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">I just also realized - would creating a cache from this gff file (using <a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a>) not be recommended?</div><span class="HOEnZb"><font color="#888888"> <br> <div><div style="font-family:helvetica,arial;font-size:13px">-Konrad</div></div></font></span><div><div class="h5"> <br><p>On September 27, 2016 at 5:16:42 AM, Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>) wrote:</p> <blockquote type="cite"><span><div><div></div><div>
<div dir="ltr">Hi Konrad,
<div><br></div>
<div>The beta ensembl-vep code [1] supports annotation directly
from a GFF file, such as the one available from the GENCODE website
[2].</div>
<div><br></div>
<div>$ curl <a href="ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz" target="_blank">ftp://ftp.sanger.ac.uk/<wbr>pub/gencode/Gencode_human/<wbr>release_25/GRCh37_mapping/<wbr>gencode.v25lift37.annotation.<wbr>gff3.gz</a>
| gzip -dc | grep -v "#" | sort -k1,1 -k4,4n -k5,5n | bgzip -c >
gencode.v25lift37.annotation.<wbr>gff3.gz</div>
<div>$ tabix -p gff gencode.v25lift37.annotation.<wbr>gff3.gz</div>
<div>$ perl <a href="http://vep.pl" target="_blank">vep.pl</a> -i variants.vcf
-gff gencode.v25lift37.<wbr>annotation.gff3.gz -fasta
homo_sapiens.fa</div>
<div><br></div>
<div>This comes with limitations as the GFF file contains only the
transcript structure and not any of the additional annotations.
However I do know of someone successfully using LOFTEE with this
exact setup.</div>
<div><br></div>
<div>Of course usual beta caveats apply, so if you do use it and
find bugs please report on the GitHub page.</div>
<div><br></div>
<div>Regards</div>
<div><br></div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
<div><br></div>
<div>[1] : <a href="https://github.com/willmclaren/ensembl-vep" target="_blank">https://github.com/<wbr>willmclaren/ensembl-vep</a></div>
<div>[2] : <a href="http://www.gencodegenes.org/releases/25lift37.html" target="_blank">http://www.gencodegenes.org/<wbr>releases/25lift37.html</a></div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 26 September 2016 at 20:40, Konrad
Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
Hi all,</div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
<br></div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
When running VEP 85 on GRCh37, I believe the process has been to
annotate against Gencode 19 (the info.txt seems to confirm this).
Realizing the ridiculousness of my request, is there any chance
there is a cache floating around for Gencode 25lift37? Would go a
long way for ExAC releases. </div>
<div><br></div>
Thanks!<span><font color="#888888"><br></font></span>
<div>
<div style="font-family:helvetica,arial;font-size:13px">
<span><font color="#888888">-Konrad</font></span></div>
</div>
</div>
<br>
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